Antibodies against signal-regulatory protein alpha and methods of use

Abstract

Provided herein, inter alia, are isolated antibodies that bind an extracellular domain of a human SIRP-α v1 polypeptide (e.g., the D1 domain), an extracellular domain of a human SIRP-α v2 polypeptide, or both. In some embodiments, the antibodies also bind an extracellular domain of a monkey SIRP-α polypeptide, an extracellular domain of a mouse SIRP-α polypeptide, an extracellular domain of a human SIRP-β polypeptide, and/or an extracellular domain of a human SIRP-γ polypeptide. In some embodiments, the antibodies block or do not binding between an extracellular domain of a human SIRP-α polypeptide and an IgSF domain of a human CD47 polypeptide, while in some embodiments, the antibodies reduce the affinity of a human SIRP-α polypeptide for binding an IgSF domain of a human CD47 polypeptide. Further provided herein are methods, polynucleotides, vectors, and host cells related thereto.

What is claimed is: 
     
       1. An isolated antibody that binds an extracellular domain of a human SIRP-α polypeptide, wherein the antibody comprises:
 (a) a heavy chain variable (VH) domain comprising:
 (i) an HVR-H1 sequence comprising the amino acid sequence of SYDMN (SEQ ID NO: 270), SYDVN (SEQ ID NO:221), or SYDLN (SEQ ID NO:313); 
 (ii) an HVR-H2 sequence comprising the amino acid sequence of LISGSGEIIYYADSVKG (SEQ ID NO: 156); and 
 (iii) an HVR-H3 sequence comprising the amino acid sequence of ENNRYRFFDD (SEQ ID NO: 157); and 
 
 (b) a light chain variable (VL) domain comprising:
 (i) an HVR-L1 sequence comprising the amino acid sequence of RASQSVYTYLA (SEQ ID NO:158); 
 (ii) an HVR-L2 sequence comprising the amino acid sequence of GASSRAT (SEQ ID NO:159); and 
 (iii) an HVR-L3 sequence comprising the amino acid sequence of QQYYDRPPLT (SEQ ID NO:160). 
 
 
     
     
       2. The antibody of  claim 1 , wherein the VH domain comprises an amino acid sequence that is at least 90% identical to the amino acid sequence of SEQ ID NO: 249, 133, 260, or 329; and the VL domain comprises an amino acid sequence that is at least 90% identical to the amino acid sequence of SEQ ID NO: 134, 250, or 251. 
     
     
       3. The antibody of  claim 1 , wherein:
 (a) the VH domain comprises the amino acid sequence of SEQ ID NO: 133, and the VL domain comprises the amino acid sequence of SEQ ID NO:134; 
 (b) the VH domain comprises the amino acid sequence of SEQ ID NO:260, and the VL domain comprises the amino acid sequence of SEQ ID NO:134; 
 (c) the VH domain comprises the amino acid sequence of SEQ ID NO:329, and the VL domain comprises the amino acid sequence of SEQ ID NO:134; 
 (d) the VH domain comprises the amino acid sequence of SEQ ID NO: 133, and the VL domain comprises the amino acid sequence of SEQ ID NO:250; 
 (e) the VH domain comprises the amino acid sequence of SEQ ID NO:260, and the VL domain comprises the amino acid sequence of SEQ ID NO:250; 
 (f) the VH domain comprises the amino acid sequence of SEQ ID NO:329, and the VL domain comprises the amino acid sequence of SEQ ID NO:250; 
 (g) the VH domain comprises the amino acid sequence of SEQ ID NO: 133, and the VL domain comprises the amino acid sequence of SEQ ID NO:251; 
 (h) the VH domain comprises the amino acid sequence of SEQ ID NO:260, and the VL domain comprises the amino acid sequence of SEQ ID NO:251; 
 (i) the VH domain comprises the amino acid sequence of SEQ ID NO:329, and the VL domain comprises the amino acid sequence of SEQ ID NO:251; 
 (j) the VH domain comprises the amino acid sequence of SEQ ID NO:249, and the VL domain comprises the amino acid sequence of SEQ ID NO:134; 
 (k) the VH domain comprises the amino acid sequence of SEQ ID NO:249, and the VL domain comprises the amino acid sequence of SEQ ID NO:250; or 
 (l) the VH domain comprises the amino acid sequence of SEQ ID NO:249, and the VL domain comprises the amino acid sequence of SEQ ID NO:251. 
 
     
     
       4. The antibody of  claim 1 , wherein the antibody enhances phagocytosis by a macrophage expressing a human SIRP-α polypeptide. 
     
     
       5. The antibody of  claim 1 , wherein the antibody enhances activation of a dendritic cell expressing a human SIRP-α polypeptide. 
     
     
       6. The antibody of  claim 1 , wherein the antibody inhibits in vivo growth of a tumor that expresses CD47. 
     
     
       7. The antibody of  claim 1 , wherein the antibody does not prevent interactions between a CD47-expressing cell and a T cell. 
     
     
       8. The antibody of  claim 1 , wherein the antibody is a monoclonal antibody. 
     
     
       9. The antibody of  claim 1 , wherein the antibody is a scFv-Fc antibody. 
     
     
       10. The antibody of  claim 1 , wherein the antibody comprises a light chain constant region comprising the amino acid sequence of SEQ ID NO:325, 326, or 426. 
     
     
       11. The antibody of  claim 1 , wherein the antibody comprises an Fc region. 
     
     
       12. The antibody of  claim 11 , wherein the antibody comprises an antibody heavy chain polypeptide that comprises the VH domain and a constant region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 320-324. 
     
     
       13. The antibody of  claim 11 , wherein the Fc region is a human Fc region selected from the group consisting of an IgG1 Fc region, an IgG2 Fc region, and an IgG4 Fc region. 
     
     
       14. The antibody of  claim 11 , wherein the Fc region comprises a human IgG1 Fc region comprising one or more mutations selected from the group consisting of L234A, L235A, G237A, and N297A, according to EU numbering. 
     
     
       15. The antibody of  claim 11 , wherein the Fc region comprises a human IgG2 Fc region comprising one or more mutations selected from the group consisting of A330S, P331S and N297A, according to EU numbering. 
     
     
       16. The antibody of  claim 11 , wherein the Fc region comprises a human IgG4 Fc region comprising one or more mutations selected from the group consisting of S228P, E233P, F234V, L235A, L235E, delG236, and N297A, according to EU numbering. 
     
     
       17. The antibody of  claim 1 , wherein the antibody is an antibody fragment selected from the group consisting of a Fab, F(ab′)2, Fab′-SH, Fv, and scFv fragment. 
     
     
       18. The antibody of  claim 1 , wherein the antibody is conjugated to a cytotoxic agent or label. 
     
     
       19. The antibody of  claim 1 , wherein the antibody is a bispecific antibody. 
     
     
       20. The antibody of  claim 19 , wherein the antibody comprises a first antigen binding domain comprising the VH and VL domain that bind an extracellular domain of a human SIRP-α polypeptide and a second antigen binding domain comprising a second VH domain and second VL domain that bind an antigen expressed by a cancer cell. 
     
     
       21. The antibody of  claim 20 , wherein the antigen expressed by the cancer cell is selected from the group consisting of CD19, CD20, CD22, CD30, CD33, CD38, CD52, CD56, CD70, CD74, CD79b, CD123, CD138, CS1/SLAMF7, Trop-2, 5T4, EphA4, BCMA, Mucin 1, Mucin 16, PD-L1, PTK7, STEAP1, Endothelin B Receptor, mesothelin, EGFRVIII, ENPP3, SLC44A4, GNMB, nectin 4, NaPi2b, LIV-1A, Guanylyl cyclase C, DLL3, EGFR, HER2, VEGF, VEGFR, integrin αVβ3, integrin α5β1, MET, IGF1R, TRAILR1, TRAILR2, RANKL, FAP, Tenascin, Le y , EpCAM, CEA, gpA33, PSMA, TAG72, a mucin, CAIX, EPHA3, folate receptor α, GD2, GD3, and an MHC/peptide complex comprising a peptide from NY-ESO-1/LAGE, SSX-2, MAGE-A3, gp100/pmel17, Melan-A/MART-1, gp75/TRP1, tyrosinase, TRP2, CEA, PSA, TAG-72, immature laminin receptor, MOK/RAGE-1, WT-1, SAP-1, BING-4, EpCAM, MUC1, PRAME, survivin, BRCA1, BRCA2, CDK4, CML66, MART-2, p53, Ras, β-catenin, TGF-βRII, HPV E6, or HPV E7. 
     
     
       22. The antibody of  claim 1 , wherein the antibody is a human antibody. 
     
     
       23. A polynucleotide encoding the antibody of  claim 1 . 
     
     
       24. A vector comprising the polynucleotide of  claim 23 . 
     
     
       25. A host cell comprising the polynucleotide of  claim 23 . 
     
     
       26. A method of producing an antibody, the method comprising culturing the host cell of  claim 25  such that the antibody that binds the extracellular domain of a human SIRP-α polypeptide is produced. 
     
     
       27. The method of  claim 26 , further comprising recovering the antibody from the host cell. 
     
     
       28. The antibody of  claim 1 , wherein the antibody binds an extracellular domain of a human SIRP-α v1 polypeptide comprising the amino acid sequence of 
       
         
           
                 
               
                   (SEQ ID NO: 5) 
                 
                   EEELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWFRGAGPGRELIY 
                 
                     
                 
                   NQKEGHFPRVTTVSDLTKRNNMDFSIRIGNITPADAGTYYCVKFRKGSPD 
                 
                     
                 
                   DVEFKSGAGTELSVRAKPS. 
                 
             
                
                
                
                
                
                
               
            
           
         
       
     
     
       29. The antibody of  claim 1 , wherein the antibody binds an extracellular domain of a human SIRP-α v2 polypeptide comprising the amino acid sequence of 
       
         
           
                 
               
                   (SEQ ID NO: 6) 
                 
                   EEELQVIQPDKSVSVAAGESAILHCTVTSLIPVGPIQWFRGAGPARELI 
                 
                     
                 
                   YNQKEGHFPRVTTVSESTKRENMDFSISISNITPADAGTYYCVKFRKGS 
                 
                     
                 
                   PDTEFKSGAGTELSVRAKPS. 
                 
             
                
                
                
                
                
                
               
            
           
         
       
     
     
       30. The antibody of  claim 1 , wherein the antibody is capable of binding an extracellular domain of a human SIRP-α v1 polypeptide comprising the amino acid sequence of EEELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRV TTVSDLTKRNNMDFSIRIGNITPADAGTYYCVKFRKGSPDDVEFKSGAGTELSVRAKPS (SEQ ID NO:5) and is capable of binding an extracellular domain of a human SIRP-α v2 polypeptide comprising the amino acid sequence of 
       
         
           
                 
               
                   (SEQ ID NO: 6) 
                 
                   EEELQVIQPDKSVSVAAGESAILHCTVTSLIPVGPIQWFRGAGPARELIY 
                 
                     
                 
                   NQKEGHFPRVTTVSESTKRENMDFSISISNITPADAGTYYCVKFRKGSPD 
                 
                     
                 
                   TEFKSGAGTELSVRAKPS. 
                 
             
                
                
                
                
                
                
               
            
           
         
       
     
     
       31. The antibody of  claim 1 , wherein the antibody binds an extracellular domain of a cynomolgus SIRP-α polypeptide comprising the amino acid sequence of SEQ ID NO:11. 
     
     
       32. The antibody of  claim 1 , wherein the antibody binds an extracellular domain of a murine SIRP-α polypeptide comprising the amino acid sequence of SEQ ID NO:7. 
     
     
       33. The antibody of  claim 1 , wherein the antibody binds the extracellular domain of a human SIRP-β polypeptide comprising the amino acid sequence of SEQ ID NO:13. 
     
     
       34. The antibody of  claim 1 , wherein the antibody does not block binding between an extracellular domain of a human SIRP-α polypeptide and an IgSF domain of a human CD47 polypeptide. 
     
     
       35. A host cell comprising the vector of  claim 24 . 
     
     
       36. A method of producing an antibody, the method comprising culturing the host cell of  claim 35  such that the antibody that binds the extracellular domain of a human SIRP-α polypeptide is produced. 
     
     
       37. The method of  claim 36 , further comprising recovering the antibody from the host cell.